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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-10-15 12:12:16 UTC
Update Date2021-09-14 15:00:41 UTC
HMDB IDHMDB0010725
Secondary Accession Numbers
  • HMDB10725
Metabolite Identification
Common Name(R)-3-Hydroxydecanoic acid
Description(R)-3-Hydroxydecanoic acid, also known as 3-HDA or myrmicacin, belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain (R)-3-Hydroxydecanoic acid exists in all eukaryotes, ranging from yeast to plants to humans. In humans, (R)-3-hydroxydecanoic acid is involved in the fatty acid biosynthesis pathway (R)-3-Hydroxydecanoic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make (R)-3-hydroxydecanoic acid a potential biomarker for the consumption of these foods (R)-3-Hydroxydecanoic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on (R)-3-Hydroxydecanoic acid.
Structure
Data?1582752866
Synonyms
ValueSource
(R)-3-HydroxydecanoateGenerator
3-HDAHMDB
3-Hydroxydecanoic acidHMDB
beta-Hydroxydecanoic acidHMDB
Myrmicacin, (+-)-isomerHMDB
Myrmicacin monosodium (+-)-isomerHMDB
3-Hydroxy-decanoic acidHMDB
Myrmicacin, (R)-isomerHMDB
MyrmicacinHMDB
Chemical FormulaC10H20O3
Average Molecular Weight188.264
Monoisotopic Molecular Weight188.141244506
IUPAC Name(3R)-3-hydroxydecanoic acid
Traditional Name(R)-3-hydroxydecanoic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(CCCCCCC)CC(O)=O
InChI Identifier
InChI=1S/C10H20O3/c1-2-3-4-5-6-7-9(11)8-10(12)13/h9,11H,2-8H2,1H3,(H,12,13)/t9-/m1/s1
InChI KeyFYSSBMZUBSBFJL-SECBINFHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct ParentMedium-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Beta-hydroxy acid
  • Hydroxy fatty acid
  • Fatty acyl
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.74 g/LALOGPS
logP10(2.6) g/LALOGPS
logP10(2.36) g/LChemAxon
logS10(-2) g/LALOGPS
pKa (Strongest Acidic)4.67ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity50.99 m³·mol⁻¹ChemAxon
Polarizability22.35 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+147.4131661259
DarkChem[M-H]-144.41831661259

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(R)-3-Hydroxydecanoic acid[H][C@@](O)(CCCCCCC)CC(O)=O2632.9Standard polar33892256
(R)-3-Hydroxydecanoic acid[H][C@@](O)(CCCCCCC)CC(O)=O1487.9Standard non polar33892256
(R)-3-Hydroxydecanoic acid[H][C@@](O)(CCCCCCC)CC(O)=O1569.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(R)-3-Hydroxydecanoic acid,1TMS,isomer #1CCCCCCC[C@H](CC(=O)O)O[Si](C)(C)C1582.5Semi standard non polar33892256
(R)-3-Hydroxydecanoic acid,1TMS,isomer #2CCCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C1570.1Semi standard non polar33892256
(R)-3-Hydroxydecanoic acid,2TMS,isomer #1CCCCCCC[C@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1665.8Semi standard non polar33892256
(R)-3-Hydroxydecanoic acid,1TBDMS,isomer #1CCCCCCC[C@H](CC(=O)O)O[Si](C)(C)C(C)(C)C1804.3Semi standard non polar33892256
(R)-3-Hydroxydecanoic acid,1TBDMS,isomer #2CCCCCCC[C@@H](O)CC(=O)O[Si](C)(C)C(C)(C)C1799.5Semi standard non polar33892256
(R)-3-Hydroxydecanoic acid,2TBDMS,isomer #1CCCCCCC[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2122.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - (R)-3-Hydroxydecanoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-007c-9200000000-f9795d95896f66d907662016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (R)-3-Hydroxydecanoic acid GC-MS (2 TMS) - 70eV, Positivesplash10-010c-9041000000-b9b51f3624f22e4b6c9d2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - (R)-3-Hydroxydecanoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 10V, Positive-QTOFsplash10-00dr-0900000000-1d9eae6ad3d5e431996b2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Positive-QTOFsplash10-0fmr-3900000000-bbd0b333dda24219033a2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Positive-QTOFsplash10-052f-9200000000-7cc23eacacf566b10ff02016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 10V, Negative-QTOFsplash10-000i-1900000000-46d09f9537cea04f6e132016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Negative-QTOFsplash10-054x-3900000000-76f4dd284af0c499a0a82016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Negative-QTOFsplash10-0a6u-9400000000-84da3410c532bb2e22732016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 10V, Negative-QTOFsplash10-000i-1900000000-2019592125745914c6e02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Negative-QTOFsplash10-0a6r-9800000000-b6a04af2348e32c411662021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Negative-QTOFsplash10-052f-9000000000-8f7fd17dc3ad7497c3772021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 10V, Positive-QTOFsplash10-009i-9800000000-2661614f9f11754f0d3a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 20V, Positive-QTOFsplash10-0a4l-9000000000-b7cbaa25fb90f53def322021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (R)-3-Hydroxydecanoic acid 40V, Positive-QTOFsplash10-0a4l-9000000000-6609ad3e1fed5bc9c4ca2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB027873
KNApSAcK IDNot Available
Chemspider ID4472223
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5312798
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Involved in transferase activity
Specific function:
Fatty acid synthetase catalyzes the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. This multifunctional protein has 7 catalytic activities and an acyl carrier protein.
Gene Name:
FASN
Uniprot ID:
P49327
Molecular weight:
273424.06